Directory mrUtilities/File/Nifti/

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justin 2012-06-13 23:13 Rev.: 2581

Check for problem opening file

2 lines of code changed in 2 files:

• mrUtilities/File/Nifti: cbiReadNifti.m (+1), cbiReadNiftiHeader.m (+1)

justin 2011-10-02 22:20 Rev.: 2353

This function would not let you save a nifti xform set to identity. This seems like a bad assumption. It is now changed so that it will set the xform as long as the qform_code or sform_code is not set to 0.

2 lines of code changed in 1 file:

• mrUtilities/File/Nifti: cbiCreateNiftiHeader.m (+2 -2)

justin 2011-09-04 22:24 Rev.: 2283

Minor, remove ver output of fileparts to avoid warning

2 lines of code changed in 2 files:

• mrUtilities/File/Nifti: cbiCreateNiftiHeader.m (+1 -1), cbiWriteNifti.m (+1 -1)

eli 2010-10-14 23:35 Rev.: 1733

modified call to fileparts on line 35 b/c the fourth output, VERSN, of FILEPARTS will be removed in a future release.

3 lines of code changed in 1 file:

• mrUtilities/File/Nifti: cbiWriteNiftiHeader.m (+3 -1)

eli 2010-10-14 23:07 Rev.: 1732

changed the call to fileparts on line 35 to only have three outputs, since fourth output, VERSN, of FILEPARTS will be removed in a future release.

1 lines of code changed in 1 file:

• mrUtilities/File/Nifti: cbiReadNiftiHeader.m (+1 -1)

justin 2010-07-16 15:54 Rev.: 1702

Returing sliceIndex of the files (this is used for checking l/r of anatomy)

18 lines of code changed in 1 file:

• mrUtilities/File/Nifti: getPermutationMatrix.m (+18 -4)

justin 2010-01-07 17:46 Rev.: 1619

allow for hard links

3 lines of code changed in 1 file:

• mrUtilities/File/Nifti: copyNiftiFile.m (+3 -3)

justin 2009-12-11 11:27 Rev.: 1576

minor: print help info instead of crashing when you call with no arguments

9 lines of code changed in 2 files:

• mrUtilities/File/Nifti: cbiWriteNifti.m (+4 -1), cbiWriteNiftiHeader.m (+5)

justin 2009-07-23 10:40 Rev.: 1518

Adding mlrImage directory and the start of some functions that should serve as a wrapper around cbiReadNifti functions. THis will give us more flexibility in the future to be nifti independent -- for example, we can write read/write wrappers so that we aren't limited by the 16bit image width/height parameters, which is a problem for the surface images that.

Also, fixed cbiReadNiftiHeader so that it doesn't dump an error when it can't load a header, but returns gracefully with a warning and an empty header structure

11 lines of code changed in 1 file:

• mrUtilities/File/Nifti: cbiReadNiftiHeader.m (+11 -5)

justin 2009-07-03 16:46 Rev.: 1497

Added checks for correct extension and to check for file existence

15 lines of code changed in 2 files:

• mrUtilities/File/Nifti: cbiReadNifti.m (+10), cbiWriteNifti.m (+5 -1)

justin 2009-01-10 07:31 Rev.: 1367

Now copies associated .mat file as well (i.e. .mat file with same stem name)

10 lines of code changed in 1 file:

• mrUtilities/File/Nifti: copyNiftiFile.m (+10 -3)

justin 2009-01-09 07:11 Rev.: 1358

optional paramter to allow linking rather than copying

14 lines of code changed in 1 file:

• mrUtilities/File/Nifti: copyNiftiFile.m (+14 -6)

justin 2009-01-08 08:03 Rev.: 1354

function to copy one nifti file to another location -- it handles the dual files correctly and checks for existence of files etc.

61 lines of code changed in 1 file:

• mrUtilities/File/Nifti: copyNiftiFile.m (new 61)

justin 2009-01-07 06:49 Rev.: 1352

Added functionality to support 1xn images where n is greater than a 16bit int width. This is useful for the surface curvature files that MLR saves. It now writes them out as a kx65535 image in which the description field holds the actualy width of the image (n). cbiRead/Write nifti can now read and write this out. Also, the old surface nifti files were based on a bit of a hack -- if the image width was 65535 it would just continue to load data, but there was no explicit setting as to what the width actually was. Those files still correctly open but the user gets an option to resave it in the new format (which is advised).

81 lines of code changed in 2 files:

• mrUtilities/File/Nifti: cbiReadNifti.m (+47 -1), cbiWriteNifti.m (+34)

justin 2008-11-25 08:15 Rev.: 1341

Some slice perscriptions were getting weird results for what happens when you click the coronal/sagittal/axial radio buttons. I think this is because the slices are tilted backwards, and the permutation logic assigns what should really be the coronal view to the axial view. I have added a fix in here, which looks for slices that are rotated in this way and fixes the permutation matrix accordingly. I am not 100% sure that this will work for all slice orientations.

30 lines of code changed in 1 file:

• mrUtilities/File/Nifti: getPermutationMatrix.m (+30 -4)

justin 2008-04-11 23:35 Rev.: 1045

print out of how much coordinates have been shifted by

3 lines of code changed in 1 file:

• mrUtilities/File/Nifti: xformSurfaceWorld2Array.m (+3)

justin 2008-04-11 12:08 Rev.: 1043

didn't need another +1 offset for C to matlab since jonas' xform from mlrXformFromHeader handles that

0 lines of code changed in 1 file:

• mrUtilities/File/Nifti: xformSurfaceWorld2Array.m (-2)

justin 2008-04-11 00:55 Rev.: 1035

implemented changes needed to handle the world2array xform that jonas' surfrelax tools assume. Basically the analyze header had fields pixdim(6:8) which is an offset and that needs to shift the origin of the coordinates in the surfaces to get them into array coordinates. This is now handled by a function xformSurfaceWorld2Array which also handles the necessary 0 to 1 based coordinate frame change. We also removed all x/y swaps which were unnecessary. loadSurfOFF was swapping xy and then we later swapped them back in loadSurface and loadFlatOFF.

6 lines of code changed in 1 file:

• mrUtilities/File/Nifti: xformSurfaceWorld2Array.m (+6 -1)

justin 2008-04-11 00:12 Rev.: 1034

function from jonas which does world2array xform for surfaces. Note that there is a minor change that allows passing in a header instead of a filename

93 lines of code changed in 1 file:

• mrUtilities/File/Nifti: mlrXFormFromHeader.m (new 93)

justin 2008-04-11 00:01 Rev.: 1032

*** empty log message ***

42 lines of code changed in 1 file:

• mrUtilities/File/Nifti: xformSurfaceWorld2Array.m (new 42)

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